amwaterhouse [Tue, 6 Dec 2005 11:03:02 +0000 (11:03 +0000)]
New help
amwaterhouse [Tue, 6 Dec 2005 09:15:56 +0000 (09:15 +0000)]
Paste this makes new sequence
amwaterhouse [Tue, 6 Dec 2005 09:15:35 +0000 (09:15 +0000)]
Size changes
amwaterhouse [Mon, 5 Dec 2005 16:30:50 +0000 (16:30 +0000)]
No more dbprefix
amwaterhouse [Mon, 5 Dec 2005 16:30:25 +0000 (16:30 +0000)]
Move lastframex when frame closes
amwaterhouse [Mon, 5 Dec 2005 16:29:55 +0000 (16:29 +0000)]
New instructions for making groups file
amwaterhouse [Mon, 5 Dec 2005 16:29:26 +0000 (16:29 +0000)]
SequenceFeature mouse over text updated
amwaterhouse [Mon, 5 Dec 2005 16:28:56 +0000 (16:28 +0000)]
Catch null colour exception
amwaterhouse [Mon, 5 Dec 2005 16:28:31 +0000 (16:28 +0000)]
Remove image import
amwaterhouse [Mon, 5 Dec 2005 16:27:49 +0000 (16:27 +0000)]
Location of protein name specified
amwaterhouse [Mon, 5 Dec 2005 13:39:56 +0000 (13:39 +0000)]
Save Feature Rendering
amwaterhouse [Mon, 5 Dec 2005 13:39:17 +0000 (13:39 +0000)]
Readjustments
amwaterhouse [Mon, 5 Dec 2005 13:39:01 +0000 (13:39 +0000)]
Allow for uniprot in name
amwaterhouse [Mon, 5 Dec 2005 13:38:42 +0000 (13:38 +0000)]
Prov not used in this version
amwaterhouse [Mon, 5 Dec 2005 13:38:26 +0000 (13:38 +0000)]
Use regex on seq names
amwaterhouse [Mon, 5 Dec 2005 13:38:08 +0000 (13:38 +0000)]
not needed
amwaterhouse [Mon, 5 Dec 2005 13:37:38 +0000 (13:37 +0000)]
Save features
amwaterhouse [Mon, 5 Dec 2005 13:28:50 +0000 (13:28 +0000)]
Save feature settings
amwaterhouse [Fri, 2 Dec 2005 17:06:51 +0000 (17:06 +0000)]
Output from newick menu item bug fixed
amwaterhouse [Fri, 2 Dec 2005 15:53:08 +0000 (15:53 +0000)]
Remove fillarc
amwaterhouse [Fri, 2 Dec 2005 15:52:51 +0000 (15:52 +0000)]
Remove comments
amwaterhouse [Fri, 2 Dec 2005 15:52:39 +0000 (15:52 +0000)]
Sequence, not SequenceI
amwaterhouse [Fri, 2 Dec 2005 15:51:58 +0000 (15:51 +0000)]
Reset frame position on startup
amwaterhouse [Fri, 2 Dec 2005 15:28:25 +0000 (15:28 +0000)]
SequenceFeatures is null by default
amwaterhouse [Fri, 2 Dec 2005 15:27:54 +0000 (15:27 +0000)]
Null pointer removed
amwaterhouse [Fri, 2 Dec 2005 15:27:35 +0000 (15:27 +0000)]
Larger for mac
amwaterhouse [Wed, 30 Nov 2005 18:14:57 +0000 (18:14 +0000)]
Only seek for sequences without features
amwaterhouse [Wed, 30 Nov 2005 18:14:21 +0000 (18:14 +0000)]
Applet changes
amwaterhouse [Wed, 30 Nov 2005 18:13:46 +0000 (18:13 +0000)]
Load pdb file with applet
amwaterhouse [Wed, 30 Nov 2005 18:13:28 +0000 (18:13 +0000)]
AppletPDBViewer needs to know type of file transfer
amwaterhouse [Wed, 30 Nov 2005 18:13:03 +0000 (18:13 +0000)]
Get viewport and seqcanvas methods
amwaterhouse [Wed, 30 Nov 2005 15:37:59 +0000 (15:37 +0000)]
Parse id before url completion
amwaterhouse [Wed, 30 Nov 2005 15:37:36 +0000 (15:37 +0000)]
REmove import
amwaterhouse [Wed, 30 Nov 2005 15:37:08 +0000 (15:37 +0000)]
Name parsing
amwaterhouse [Wed, 30 Nov 2005 15:36:52 +0000 (15:36 +0000)]
Make dataset with getName, not displayid
amwaterhouse [Wed, 30 Nov 2005 15:36:19 +0000 (15:36 +0000)]
REpaint after sequence col selected
amwaterhouse [Wed, 30 Nov 2005 15:07:38 +0000 (15:07 +0000)]
GetResidueBoxColour needs no colourscheme
amwaterhouse [Wed, 30 Nov 2005 15:07:09 +0000 (15:07 +0000)]
Parse id before showing uniprot link
amwaterhouse [Wed, 30 Nov 2005 15:06:14 +0000 (15:06 +0000)]
Exact mapping for applet as well
amwaterhouse [Wed, 30 Nov 2005 15:05:57 +0000 (15:05 +0000)]
Remove deletebonds
amwaterhouse [Wed, 30 Nov 2005 15:05:12 +0000 (15:05 +0000)]
TER flag added
amwaterhouse [Tue, 29 Nov 2005 18:02:32 +0000 (18:02 +0000)]
Retrieve protein name
amwaterhouse [Tue, 29 Nov 2005 18:01:43 +0000 (18:01 +0000)]
Add your own label
amwaterhouse [Tue, 29 Nov 2005 18:01:16 +0000 (18:01 +0000)]
No need for method or chain
amwaterhouse [Tue, 29 Nov 2005 18:00:55 +0000 (18:00 +0000)]
Read in Protein name
amwaterhouse [Tue, 29 Nov 2005 18:00:30 +0000 (18:00 +0000)]
Uniprot retrieves features from XML
amwaterhouse [Tue, 29 Nov 2005 17:59:53 +0000 (17:59 +0000)]
Parse id before making URL
amwaterhouse [Tue, 29 Nov 2005 17:59:29 +0000 (17:59 +0000)]
Features added removed from alignment
amwaterhouse [Tue, 29 Nov 2005 17:58:40 +0000 (17:58 +0000)]
ExactMapping is in pdbchain
amwaterhouse [Tue, 29 Nov 2005 17:58:05 +0000 (17:58 +0000)]
Wait till visiblebonds!=null before painting
amwaterhouse [Tue, 29 Nov 2005 17:57:41 +0000 (17:57 +0000)]
Save features and pdbids
amwaterhouse [Tue, 29 Nov 2005 17:57:00 +0000 (17:57 +0000)]
Save features and pdbids in jar file
amwaterhouse [Mon, 28 Nov 2005 17:15:29 +0000 (17:15 +0000)]
new Implementation for getting colour quickly
amwaterhouse [Mon, 28 Nov 2005 17:15:06 +0000 (17:15 +0000)]
Correction for feature rendering
amwaterhouse [Mon, 28 Nov 2005 17:14:49 +0000 (17:14 +0000)]
Mapping now performed in PDBChain
amwaterhouse [Mon, 28 Nov 2005 17:14:23 +0000 (17:14 +0000)]
wrapped alignment 1 larger
amwaterhouse [Mon, 28 Nov 2005 17:13:54 +0000 (17:13 +0000)]
Mapping for alignment added to residue
amwaterhouse [Fri, 25 Nov 2005 17:57:57 +0000 (17:57 +0000)]
Must follow alignmentPosition
amwaterhouse [Fri, 25 Nov 2005 17:57:37 +0000 (17:57 +0000)]
Comment out test lines
amwaterhouse [Fri, 25 Nov 2005 17:57:15 +0000 (17:57 +0000)]
Dont request focus
amwaterhouse [Fri, 25 Nov 2005 17:57:01 +0000 (17:57 +0000)]
-1 adjust
amwaterhouse [Fri, 25 Nov 2005 17:56:20 +0000 (17:56 +0000)]
Read in Hetatms, allow for models, highlight in canvas
amwaterhouse [Fri, 25 Nov 2005 16:08:06 +0000 (16:08 +0000)]
Correct mapping for pdb file
amwaterhouse [Fri, 25 Nov 2005 16:07:17 +0000 (16:07 +0000)]
Spinner images
amwaterhouse [Thu, 24 Nov 2005 12:16:09 +0000 (12:16 +0000)]
Don't parse input id, leave it as it is
amwaterhouse [Thu, 24 Nov 2005 12:14:53 +0000 (12:14 +0000)]
New EBI WS implementation
amwaterhouse [Thu, 24 Nov 2005 12:14:08 +0000 (12:14 +0000)]
New WSWUBlast Client files
amwaterhouse [Fri, 18 Nov 2005 11:37:05 +0000 (11:37 +0000)]
Add PDB accession to new sequence
amwaterhouse [Fri, 18 Nov 2005 11:36:27 +0000 (11:36 +0000)]
Allow single line BLC files
amwaterhouse [Fri, 18 Nov 2005 11:36:07 +0000 (11:36 +0000)]
Use PDB column format
amwaterhouse [Fri, 18 Nov 2005 10:25:01 +0000 (10:25 +0000)]
Allow for 1 line BLC files
amwaterhouse [Fri, 18 Nov 2005 10:24:38 +0000 (10:24 +0000)]
Parse name from last index of /
amwaterhouse [Fri, 18 Nov 2005 10:24:06 +0000 (10:24 +0000)]
Use full name in dataset creation
amwaterhouse [Fri, 18 Nov 2005 09:59:46 +0000 (09:59 +0000)]
Show error message outside thread loop
amwaterhouse [Thu, 17 Nov 2005 18:18:55 +0000 (18:18 +0000)]
Hidden tabs and vamsas refs for beta release
amwaterhouse [Thu, 17 Nov 2005 18:16:24 +0000 (18:16 +0000)]
Initial col is light gray
amwaterhouse [Thu, 17 Nov 2005 15:33:26 +0000 (15:33 +0000)]
Graphics must be set from nullFrame
amwaterhouse [Thu, 17 Nov 2005 15:21:08 +0000 (15:21 +0000)]
No more isOverview
amwaterhouse [Thu, 17 Nov 2005 15:20:31 +0000 (15:20 +0000)]
If overview is visible, update it
amwaterhouse [Thu, 17 Nov 2005 15:20:07 +0000 (15:20 +0000)]
no more show translation
amwaterhouse [Thu, 17 Nov 2005 15:19:20 +0000 (15:19 +0000)]
Hide Tab settings for build
amwaterhouse [Thu, 17 Nov 2005 15:18:52 +0000 (15:18 +0000)]
Use setRGB rather than color, fillrect
amwaterhouse [Thu, 17 Nov 2005 15:18:07 +0000 (15:18 +0000)]
Move start and end before parsing name
amwaterhouse [Thu, 17 Nov 2005 15:17:40 +0000 (15:17 +0000)]
Hide vamsas settings for build
amwaterhouse [Thu, 17 Nov 2005 15:17:08 +0000 (15:17 +0000)]
Now outputs features and groups, and wrapped alignment limits
amwaterhouse [Thu, 17 Nov 2005 15:16:48 +0000 (15:16 +0000)]
Optimized Overview
amwaterhouse [Thu, 17 Nov 2005 15:16:19 +0000 (15:16 +0000)]
Use stringbuffer, not string+
amwaterhouse [Thu, 17 Nov 2005 15:14:10 +0000 (15:14 +0000)]
Remove system.out
amwaterhouse [Wed, 16 Nov 2005 17:02:14 +0000 (17:02 +0000)]
Highlight doesnt use offset
amwaterhouse [Wed, 16 Nov 2005 16:42:45 +0000 (16:42 +0000)]
Don't initialise a char in findIndex
amwaterhouse [Wed, 16 Nov 2005 16:42:08 +0000 (16:42 +0000)]
Don't set chain colours in hashtable
amwaterhouse [Wed, 16 Nov 2005 16:41:35 +0000 (16:41 +0000)]
Highlight from alignment
amwaterhouse [Wed, 16 Nov 2005 16:41:08 +0000 (16:41 +0000)]
No more myAtom, Highlight from alignment
amwaterhouse [Wed, 16 Nov 2005 16:40:40 +0000 (16:40 +0000)]
no need for myAtom
amwaterhouse [Wed, 16 Nov 2005 16:40:02 +0000 (16:40 +0000)]
Parsing updates
amwaterhouse [Wed, 16 Nov 2005 16:39:08 +0000 (16:39 +0000)]
Not used
amwaterhouse [Tue, 15 Nov 2005 11:13:36 +0000 (11:13 +0000)]
Keep all public methods
amwaterhouse [Tue, 15 Nov 2005 11:13:10 +0000 (11:13 +0000)]
No radio buttons in applet
amwaterhouse [Tue, 15 Nov 2005 11:11:49 +0000 (11:11 +0000)]
Dont use this yet
amwaterhouse [Tue, 15 Nov 2005 11:10:56 +0000 (11:10 +0000)]
Dont use myGraphics
git://source.jalview.org / jalview.git / log